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Crystal structure of queuine salvage enzyme DUF2419, wild-type (non-His6x tagged)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7U07
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.2M Sodium thiocynate, 20% PEG3350, pH 6.9
Crystal Properties Matthews coefficient Solvent content 4.65 73.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.159 α = 90 b = 95.159 β = 90 c = 129.32 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2022-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.3 42 100 0.265 0.279 0.086 3.6 10.3 30413
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 99.9 6.599 6.971 2.225 0.309 9.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7U07 2.31 41.24 24343 1317 84.44 0.1518 0.1505 0.1619 0.1746 0.1843 RANDOM 38.493
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -1.14 -0.57 -1.14 3.7
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 43.912 r_dihedral_angle_2_deg 30.46 r_sphericity_bonded 22.855 r_dihedral_angle_3_deg 18.155 r_dihedral_angle_4_deg 18.106 r_dihedral_angle_1_deg 5.447 r_rigid_bond_restr 1.483 r_angle_refined_deg 1.021 r_angle_other_deg 0.783 r_chiral_restr 0.041
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 43.912 r_dihedral_angle_2_deg 30.46 r_sphericity_bonded 22.855 r_dihedral_angle_3_deg 18.155 r_dihedral_angle_4_deg 18.106 r_dihedral_angle_1_deg 5.447 r_rigid_bond_restr 1.483 r_angle_refined_deg 1.021 r_angle_other_deg 0.783 r_chiral_restr 0.041 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2530 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction PHENIX phasing